NM_015404.4(WHRN):c.1232C>T (p.Ser411Phe) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 10, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV002025864.4

Allele description [Variation Report for NM_015404.4(WHRN):c.1232C>T (p.Ser411Phe)]

NM_015404.4(WHRN):c.1232C>T (p.Ser411Phe)

Gene:

WHRN:whirlin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q32

Genomic location:

Preferred name:

NM_015404.4(WHRN):c.1232C>T (p.Ser411Phe)

HGVS:

NC_000009.12:g.114424518G>A
NG_016700.1:g.85939C>T
NM_001083885.3:c.83C>T
NM_001173425.2:c.1232C>T
NM_001346890.1:c.179C>T
NM_015404.4:c.1232C>TMANE SELECT
NP_001077354.2:p.Ser28Phe
NP_001166896.1:p.Ser411Phe
NP_001333819.1:p.Ser60Phe
NP_056219.3:p.Ser411Phe
LRG_1094t1:c.1232C>T
LRG_1094:g.85939C>T
LRG_1094p1:p.Ser411Phe
NC_000009.11:g.117186798G>A

Protein change:

S28F

Links:

dbSNP: rs1836632084

NCBI 1000 Genomes Browser:

rs1836632084

Molecular consequence:

NM_001083885.3:c.83C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001173425.2:c.1232C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001346890.1:c.179C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_015404.4:c.1232C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Mus musculus RIKEN cDNA 5033414D02 gene, mRNA (cDNA clone MGC:37072 IMAGE:495110...
Mus musculus RIKEN cDNA 5033414D02 gene, mRNA (cDNA clone MGC:37072 IMAGE:4951101), complete cds
gi|19354450|gb|BC024953.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002291510	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 10, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002291510

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 10, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002291510.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This sequence change replaces serine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 411 of the WHRN protein (p.Ser411Phe). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with WHRN-related conditions. ClinVar contains an entry for this variant (Variation ID: 1504000). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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